Sequencing depth
tibble(metric=c("Total GB", "Total reads", "Average GB", "Average reads"),
value=unlist(c(round(all_data %>% summarise(sum(bases_pre_fastp)) / 1000000000,2),
round(all_data %>% summarise(sum(bases_pre_fastp)) / 300,2),
paste0(round(all_data %>% summarise(mean(bases_pre_fastp)) / 1000000000,2),"±",round(all_data %>% summarise(sd(bases_pre_fastp)) / 1000000000,2)),
paste0(round(all_data %>% summarise(mean(bases_pre_fastp)) / 300,0),"±",round(all_data %>% summarise(sd(bases_pre_fastp)) / 300,0))))
) %>%
tt()
tinytable_22phca5lqtoxf6vp2bs4
| metric |
value |
| Total GB |
937.37 |
| Total reads |
3124578099 |
| Average GB |
5.18±2.46 |
| Average reads |
17262862±8195554 |
all_data %>%
group_by(Taxon,Extraction) %>%
summarise(value = sprintf("%.1f±%.1f", mean(bases_post_fastp / 1000000000), sd(bases_post_fastp / 1000000000))) %>%
pivot_wider(names_from = Extraction, values_from = value) %>%
tt(caption = "Mean and standard deviation of sequencing depth (GB)")
tinytable_u5z5i4ahkbwpo2xh3ryy
Mean and standard deviation of sequencing depth (GB)
| Taxon |
ZYMO |
DREX |
EHEX |
| Amphibian |
4.0±1.6 |
3.2±2.1 |
4.7±0.3 |
| Reptile |
6.1±2.2 |
5.7±1.3 |
5.0±1.8 |
| Mammal |
5.4±3.2 |
4.6±2.0 |
3.8±2.2 |
| Bird |
3.9±1.8 |
4.2±2.4 |
3.1±1.9 |
| Control |
0.0±0.0 |
0.5±0.6 |
2.1±2.7 |
all_data %>%
select(Library,Species,Extraction,bases_pre_fastp,Taxon) %>%
mutate(bases_pre_fastp=bases_pre_fastp/1000000000) %>%
unique() %>%
ggplot(aes(x=Extraction,y=bases_pre_fastp, color=Species, group=Extraction)) +
geom_boxplot(outlier.shape = NA, fill="#f4f4f4", color="#8c8c8c") +
geom_jitter() +
scale_color_manual(values=vertebrate_colors) +
facet_grid(. ~ Taxon, scales = "free") +
theme_minimal() +
labs(y="Sequencing depth (Gb)",x="Extraction method")

all_data %>%
filter(Taxon != "Control") %>%
lmerTest::lmer(bases_post_fastp ~ Extraction + (1 | Sample) + (1 | Species), data = ., REML = FALSE) %>%
broom.mixed::tidy() %>%
tt()
tinytable_ruzsab9tfj2udsw4p1ql
| effect |
group |
term |
estimate |
std.error |
statistic |
df |
p.value |
| fixed |
NA |
(Intercept) |
4808156823 |
382290022 |
12.577249 |
1.711860e+01 |
4.477658e-10 |
| fixed |
NA |
ExtractionDREX |
-485437083 |
283030980 |
-1.715138 |
4.392525e+21 |
8.632000e-02 |
| fixed |
NA |
ExtractionEHEX |
-474572486 |
284400639 |
-1.668676 |
1.443430e+09 |
9.518163e-02 |
| ran_pars |
Sample |
sd__(Intercept) |
1407267695 |
NA |
NA |
NA |
NA |
| ran_pars |
Species |
sd__(Intercept) |
508228832 |
NA |
NA |
NA |
NA |
| ran_pars |
Residual |
sd__Observation |
1524168473 |
NA |
NA |
NA |
NA |
Quality-filtering
all_data %>%
mutate(qf_bases=bases_post_fastp/bases_pre_fastp*100) %>%
group_by(Taxon,Extraction) %>%
summarise(value = sprintf("%.1f±%.1f", mean(qf_bases), sd(qf_bases))) %>%
pivot_wider(names_from = Extraction, values_from = value) %>%
tt(caption = "Mean and standard deviation of quality-filtered proportion of reads")
tinytable_io3vh2vpezfhx7lx22uw
Mean and standard deviation of quality-filtered proportion of reads
| Taxon |
ZYMO |
DREX |
EHEX |
| Amphibian |
84.7±1.2 |
91.7±3.7 |
87.6±2.9 |
| Reptile |
89.9±6.3 |
90.5±7.1 |
88.3±7.2 |
| Mammal |
91.9±2.3 |
89.5±4.7 |
91.2±1.9 |
| Bird |
70.9±16.1 |
70.3±23.0 |
70.2±14.7 |
| Control |
3.3±2.3 |
9.8±11.5 |
27.5±3.4 |
all_data %>%
mutate(qf_bases=bases_post_fastp/bases_pre_fastp*100) %>%
select(Library,Species,Extraction,qf_bases,Taxon) %>%
unique() %>%
ggplot(aes(x=Extraction,y=qf_bases, color=Species, group=Extraction)) +
geom_boxplot(outlier.shape = NA, fill="#f4f4f4", color="#8c8c8c") +
geom_jitter() +
scale_color_manual(values=vertebrate_colors) +
facet_grid(. ~ Taxon, scales = "free") +
theme_minimal() +
labs(y="High-quality data (%)",x="Extraction method")

all_data %>%
mutate(qf_bases=bases_post_fastp/bases_pre_fastp*100) %>%
filter(Taxon != "Control") %>%
lmerTest::lmer(qf_bases ~ Extraction + (1 | Sample) + (1 | Species), data = ., REML = FALSE) %>%
broom.mixed::tidy() %>%
tt()
tinytable_5m1xqtmdipuzprxp5niz
| effect |
group |
term |
estimate |
std.error |
statistic |
df |
p.value |
| fixed |
NA |
(Intercept) |
83.056667 |
3.229677 |
25.7167105 |
12.92142 |
1.758335e-12 |
| fixed |
NA |
ExtractionDREX |
1.811218 |
1.262245 |
1.4349184 |
145.69071 |
1.534536e-01 |
| fixed |
NA |
ExtractionEHEX |
0.572778 |
1.268390 |
0.4515789 |
145.71392 |
6.522438e-01 |
| ran_pars |
Sample |
sd__(Intercept) |
7.418800 |
NA |
NA |
NA |
NA |
| ran_pars |
Species |
sd__(Intercept) |
9.356829 |
NA |
NA |
NA |
NA |
| ran_pars |
Residual |
sd__Observation |
6.797395 |
NA |
NA |
NA |
NA |